Python

The steinbock framework can be used programmatically using the steinbock Python package.

In this section, the installation of the steinbock Python package is described.

For scripting use only

Installing/using the steinbock Python package directly is not recommended for regular users. Please use the steinbock Docker containers instead.

Requirements

Python 3.8 or newer

Tested versions of Python package dependencies can be found in requirements.txt.

Installation

The steinbock Python package can be installed from PyPI as follows:

pip install steinbock

The following extras are available:

• imc to enable IMC preprocessing functionality
• deepcell to enable DeepCell segmentation functionality

To install all extras, use the all extra:

pip install "steinbock[all]"

Package version conflics

Some of the dependencies of steinbock are incompatible due to different version requirements. As a workaround, use the following strategy for installing tested combinations of package versions:

# choose between one of the following:
# pip install --upgrade -r requirements_deepcell.txt
# pip install --upgrade -r requirements_deepcell-gpu.txt
pip install --no-deps deepcell==0.12.2
pip install --upgrade -r requirements.txt
pip install --no-deps "steinbock[all]"

Usage

Please refer to Python usage for usage instructions.